The invention discloses a roof rainwater source clean storage and seepage device based on the sponge city concept and a running method, relates to the field of rainwater source emission reduction and water resource protection, and discloses a technology suitable for clean collection of roof rainwater and conservation of underground water. The roof rainwater source clean storage and seepage device comprises a rainwater flow dividing tank, a rainwater flow abandoning tank, a water storage tank, an underground water conservation system and a control system. The control system can receive signals of a water quality sensor and an illumination sensor and send control instructions to an electric three-way valve and a valve of a flow abandoning hole. The roof rainwater source clean storage and seepage device has the functions and the advantages of rainwater separation and flow division, rainwater storage and accumulation and underground water clean conservation, is beneficial for reducing urban runoff pollution load, relieving drainage pressure on a city pipe network and reducing flood disasters and has great significance in improving the urban ecological water environment, relieving urban water resource shortage and promoting the harmonious development between human and nature.